I am considering the set of all finite and binary strings. In the following I am interested on the number $N(m,k,r)$ of strings with length $m$ and Hamming weight $r$ which do not contain $k$ consecutive zeros.
The Hamming weight $r$ is defined as the number of non-zero positions in a string.
Example: The binary string $x=1001101$ is given. The Hamming weight of $x$ is $r=4$, since $x$ contains 4 non-zero entries.
Is there a general formulary for computing $N(m,k,r)$?

Let $N(m,k,r)$ denote the number of binary strings with length $m$ and Hamming weight $r$ which do not contain zero-runs of length $k$.
In order to determine the number $N(m,k,r)$ we consider words with no consecutive equal characters at all.
These words are called Smirnov words or Carlitz words. (See example III.24 Smirnov words from Analytic Combinatorics by Philippe Flajolet and Robert Sedgewick for more information.)
A generating function for the number of Smirnov words over a binary alphabet is given by \begin{align*} \left(1-\frac{2z}{1+z}\right)^{-1}\tag{2} \end{align*}
We denote with $[z^n]$ the coefficient of $z^n$ in a series.
According to the factor $(1-z^k)$ in (5) we split the expression into two sums.
Comment:
In (6) we use the linearity of the coefficient of operator and apply the rule $[z^{p-q}]G(z)=[z^p]z^{q}G(z)$. We also set the upper limit of the sum to $m$ since the exponent of $z^{m-j}$ is non-negative.
In (7) we change the order of summation $j\rightarrow m-j$.
In (8) we note the exponent of $z$ has to be a multiple of $k$ due to the factor $z^{kl}$ in the inner sum. We set $j\rightarrow kj$ accordingly.
In (9) we select the coefficient of $z^{kj}$.
In (10) we do a similar job with $[t^r]$ as we did with $[z^m]$ in (6).
In (11) we select the coefficient of $t^{r-j}$.
Finally we look at an example.
Note: Here is some more detailed information to (6) due to OPs comment \begin{align*} \color{blue}{[z^mt^r]}&\color{blue}{\sum_{j=0}^\infty z^j\left((t+1)-tz^k\right)^j}\\ &=[t^r]\sum_{j=0}^m[z^m]z^j\left((t+1)-tz^k\right)^j\\ &=[t^r]\sum_{j=0}^m[z^m]z^j\left(-tz^k+(t+1)\right)^j\\ &=[t^r]\sum_{j=0}^m[z^m]z^j\sum_{l=0}^j\binom{j}{l}(-tz^k)^l(t+1)^{j-l}\\ &=[t^r]\sum_{j=0}^m[z^{m-j}]\sum_{l=0}^j\binom{j}{l}(-1)^lt^lz^{kl}(t+1)^{j-l}\tag{6}\\ \end{align*}